The Scorch Trials theme

I still have not yet completed the book The Scorch Trials, but I think I have read enough to figure out the theme. What I think the theme is that everything is not as it seems. This is because Theresa, which is one of Thomas' best friends throughout the first book, makes him think she still likes him, but betrays him and kidnaps him in the part of the book I am at. She beat him up for trying to talk and threatens to kill him. Also, when Thomas gets an infected wound, he wakes up in a ship, but soon goes back to the wasteland he is traveling to. Over the course of the book, Thomas has found out that he is in a part of another trial, went through an extremely hot desert and met two people whom he thinks have the flare. Things such as what I have described have also happened over the course of the book, so that's what I have read so far. Still an interesting book, I'm about 100 pages from the end and I'll keep updating until then.